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Abedini SS, Akhavantabasi S, Liang Y, Heng JIT, Alizadehsani R, Dehzangi I, Bauer DC, Alinejad-Rokny H. A critical review of the impact of candidate copy number variants on autism spectrum disorder. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 794:108509. [PMID: 38977176 DOI: 10.1016/j.mrrev.2024.108509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/14/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder (NDD) influenced by genetic, epigenetic, and environmental factors. Recent advancements in genomic analysis have shed light on numerous genes associated with ASD, highlighting the significant role of both common and rare genetic mutations, as well as copy number variations (CNVs), single nucleotide polymorphisms (SNPs) and unique de novo variants. These genetic variations disrupt neurodevelopmental pathways, contributing to the disorder's complexity. Notably, CNVs are present in 10 %-20 % of individuals with autism, with 3 %-7 % detectable through cytogenetic methods. While the role of submicroscopic CNVs in ASD has been recently studied, their association with genomic loci and genes has not been thoroughly explored. In this review, we focus on 47 CNV regions linked to ASD, encompassing 1632 genes, including protein-coding genes and long non-coding RNAs (lncRNAs), of which 659 show significant brain expression. Using a list of ASD-associated genes from SFARI, we detect 17 regions harboring at least one known ASD-related protein-coding gene. Of the remaining 30 regions, we identify 24 regions containing at least one protein-coding gene with brain-enriched expression and a nervous system phenotype in mouse mutants, and one lncRNA with both brain-enriched expression and upregulation in iPSC to neuron differentiation. This review not only expands our understanding of the genetic diversity associated with ASD but also underscores the potential of lncRNAs in contributing to its etiology. Additionally, the discovered CNVs will be a valuable resource for future diagnostic, therapeutic, and research endeavors aimed at prioritizing genetic variations in ASD.
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Affiliation(s)
- Seyedeh Sedigheh Abedini
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; School of Biotechnology & Biomolecular Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shiva Akhavantabasi
- Department of Molecular Biology and Genetics, Yeni Yuzyil University, Istanbul, Turkey; Ghiaseddin Jamshid Kashani University, Andisheh University Town, Danesh Blvd, 3441356611, Abyek, Qazvin, Iran
| | - Yuheng Liang
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julian Ik-Tsen Heng
- Curtin Health Innovation Research Institute, Curtin University, Bentley 6845, Australia
| | - Roohallah Alizadehsani
- Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria, Australia
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA
| | - Denis C Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Applied BioSciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, Australia
| | - Hamid Alinejad-Rokny
- UNSW BioMedical Machine Learning Lab (BML), The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW 2052, Australia; Tyree Institute of Health Engineering (IHealthE), UNSW Sydney, Sydney, NSW 2052, Australia.
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2
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Capp JP, Catania F, Thomas F. From genetic mosaicism to tumorigenesis through indirect genetic effects. Bioessays 2024; 46:e2300238. [PMID: 38736323 DOI: 10.1002/bies.202300238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Abstract
Genetic mosaicism has long been linked to aging, and several hypotheses have been proposed to explain the potential connections between mosaicism and susceptibility to cancer. It has been proposed that mosaicism may disrupt tissue homeostasis by affecting intercellular communications and releasing microenvironmental constraints within tissues. The underlying mechanisms driving these tissue-level influences remain unidentified, however. Here, we present an evolutionary perspective on the interplay between mosaicism and cancer, suggesting that the tissue-level impacts of genetic mosaicism can be attributed to Indirect Genetic Effects (IGEs). IGEs can increase the level of cellular stochasticity and phenotypic instability among adjacent cells, thereby elevating the risk of cancer development within the tissue. Moreover, as cells experience phenotypic changes in response to challenging microenvironmental conditions, these changes can initiate a cascade of nongenetic alterations, referred to as Indirect non-Genetic Effects (InGEs), which in turn catalyze IGEs among surrounding cells. We argue that incorporating both InGEs and IGEs into our understanding of the process of oncogenic transformation could trigger a major paradigm shift in cancer research with far-reaching implications for practical applications.
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Affiliation(s)
- Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Francesco Catania
- Institute of Environmental Radioactivity, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Frédéric Thomas
- CREEC, UMR IRD 224-CNRS 5290-University of Montpellier, Montpellier, France
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3
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Morison LD, Kennis MGP, Rots D, Bouman A, Kummeling J, Palmer E, Vogel AP, Liegeois F, Brignell A, Srivastava S, Frazier Z, Milnes D, Goel H, Amor DJ, Scheffer IE, Kleefstra T, Morgan AT. Expanding the phenotype of Kleefstra syndrome: speech, language and cognition in 103 individuals. J Med Genet 2024; 61:578-585. [PMID: 38290825 PMCID: PMC11148766 DOI: 10.1136/jmg-2023-109702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024]
Abstract
OBJECTIVES Speech and language impairments are core features of the neurodevelopmental genetic condition Kleefstra syndrome. Communication has not been systematically examined to guide intervention recommendations. We define the speech, language and cognitive phenotypic spectrum in a large cohort of individuals with Kleefstra syndrome. METHOD 103 individuals with Kleefstra syndrome (40 males, median age 9.5 years, range 1-43 years) with pathogenic variants (52 9q34.3 deletions, 50 intragenic variants, 1 balanced translocation) were included. Speech, language and non-verbal communication were assessed. Cognitive, health and neurodevelopmental data were obtained. RESULTS The cognitive spectrum ranged from average intelligence (12/79, 15%) to severe intellectual disability (12/79, 15%). Language ability also ranged from average intelligence (10/90, 11%) to severe intellectual disability (53/90, 59%). Speech disorders occurred in 48/49 (98%) verbal individuals and even occurred alongside average language and cognition. Developmental regression occurred in 11/80 (14%) individuals across motor, language and psychosocial domains. Communication aids, such as sign and speech-generating devices, were crucial for 61/103 (59%) individuals including those who were minimally verbal, had a speech disorder or following regression. CONCLUSIONS The speech, language and cognitive profile of Kleefstra syndrome is broad, ranging from severe impairment to average ability. Genotype and age do not explain the phenotypic variability. Early access to communication aids may improve communication and quality of life.
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Affiliation(s)
- Lottie D Morison
- Speech and Language, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Audiology and Speech Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Milou G P Kennis
- Department of Clinical Genetics, Radboudumc, Nijmegen, Netherlands
| | - Dmitrijs Rots
- Department of Clinical Genetics, Erasmus MC, Rotterdam, Netherlands
| | - Arianne Bouman
- Department of Clinical Genetics, Radboudumc, Nijmegen, Netherlands
| | - Joost Kummeling
- Department of Clinical Genetics, Radboudumc, Nijmegen, Netherlands
| | - Elizabeth Palmer
- Sydney Children's Hospital Network, Randwick, New South Wales, Australia
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Adam P Vogel
- Department of Audiology and Speech Pathology, The University of Melbourne, Melbourne, Victoria, Australia
- Redenlab, Melbourne, Victoria, Australia
| | - Frederique Liegeois
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Amanda Brignell
- Department of Paediatrics, Monash University, Clayton, Victoria, Australia
- Department of Developmental Paediatrics, Monash Children's Hospital, Clayton, Victoria, Australia
| | | | - Zoe Frazier
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Di Milnes
- Genetic Health Queensland, Herston, Queensland, Australia
| | - Himanshu Goel
- Hunter Genetics, Waratah, New South Wales, Australia
| | - David J Amor
- Speech and Language, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Paediatrics, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Ingrid E Scheffer
- Melbourne Brain Centre, Austin Health, Heidelberg, Victoria, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Tjitske Kleefstra
- Department of Clinical Genetics, Radboudumc, Nijmegen, Netherlands
- Department of Clinical Genetics, Erasmus MC, Rotterdam, Netherlands
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Audiology and Speech Pathology, The University of Melbourne, Melbourne, Victoria, Australia
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Dubey S, Ghosh R, Dubey MJ, Das S, Chakraborty AP, Santra A, Dutta A, Roy D, Pandit A, Roy BK, Das G, Benito-León J. Psychosocial Basis of Human Sufferings and Poverty in Patients with Neurological and Psychiatric Disorders. MEDICAL RESEARCH ARCHIVES 2023; 11:3919. [PMID: 37641666 PMCID: PMC10461571 DOI: 10.18103/mra.v11i5.3919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Neurological disorders and psychiatric ailments often lead to cognitive disabilities and low attainment of education, pivoting misconceptions, myths, and misbeliefs. Poverty and low educational attainment are intriguingly associated with poor awareness and perception of these diseases that add to the suffering. Poverty goes parallel with a low level of education and is intricately associated with neuropsychiatric ailments, which have the potential to spread transgenerationally. Robust education policies, proper government rules and regulations against the spread of disease-related myths and misconceptions, uplifting medical education in its true sense, voices against consanguinity, and programs to raise scientific perception about diseases can help to throw light at the end of this dark tunnel. In this article, the authors intend to 1) decipher the potential psychosocial basis of human suffering and poverty in patients with neurological and psychiatric disorders, and 2) discuss the apropos way-outs that would potentially mitigate suffering, and alleviate the economic burden and cognitive disabilities of families with neuropsychiatric diseases.
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Affiliation(s)
- Souvik Dubey
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Ritwik Ghosh
- Department of General Medicine, Burdwan Medical College, and Hospital, Burdwan, West Bengal, India
| | - Mahua Jana Dubey
- Department of Psychiatry, Berhampur Mental Hospital, Berhampur, West Bengal, India
| | - Shambaditya Das
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Arka Prava Chakraborty
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Arindam Santra
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Ajitava Dutta
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Dipayan Roy
- Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India
- School of Humanities, Indira Gandhi National Open University (IGNOU), New Delhi, India
| | - Alak Pandit
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Biman Kanti Roy
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Gautam Das
- Department of Neuromedicine, Bangur Institute of Neurosciences (BIN), Kolkata, West Bengal, India
| | - Julián Benito-León
- Department of Neurology, University Hospital “12 de Octubre”, Madrid, Spain
- Research Institute (i+12), University Hospital “12 de Octubre”, Madrid, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
- Department of Medicine, Complutense University, Madrid, Spain
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5
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Alsaqati M, Davis BA, Wood J, Jones MM, Jones L, Westwood A, Petter O, Isles AR, Linden D, Van den Bree M, Owen M, Hall J, Harwood AJ. NRSF/REST lies at the intersection between epigenetic regulation, miRNA-mediated gene control and neurodevelopmental pathways associated with Intellectual disability (ID) and Schizophrenia. Transl Psychiatry 2022; 12:438. [PMID: 36216811 PMCID: PMC9551101 DOI: 10.1038/s41398-022-02199-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic evidence indicates disrupted epigenetic regulation as a major risk factor for psychiatric disorders, but the molecular mechanisms that drive this association remain to be determined. EHMT1 is an epigenetic repressor that is causal for Kleefstra Syndrome (KS), a genetic disorder linked with neurodevelopmental disorders and associated with schizophrenia. Here, we show that reduced EHMT1 activity decreases NRSF/REST protein leading to abnormal neuronal gene expression and progression of neurodevelopment in human iPSC. We further show that EHMT1 regulates NRSF/REST indirectly via repression of miRNA and leads to aberrant neuronal gene regulation and neurodevelopment timing. Expression of a NRSF/REST mRNA that lacks the miRNA-binding sites restores neuronal gene regulation to EHMT1 deficient cells. Significantly, the EHMT1-regulated miRNA gene set not only controls NRSF/REST but is enriched for association for Intellectual Disability (ID) and schizophrenia. This reveals a broad molecular interaction between H3K9 demethylation, NSRF/REST regulation and risk for ID and Schizophrenia.
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Affiliation(s)
- Mouhamed Alsaqati
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences (DPMCN), School of Medicine, Cardiff University, Cardiff, UK.,School of Pharmacy, KGVI Building, Newcastle University, Newcastle Upon Tyne, NE1 4LF, UK
| | - Brittany A Davis
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,Lieber Institute for Brain Development, Johns Hopkins Medical Campus & Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jamie Wood
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Megan M Jones
- School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Lora Jones
- School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Aishah Westwood
- School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK
| | - Olena Petter
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK
| | - Anthony R Isles
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences (DPMCN), School of Medicine, Cardiff University, Cardiff, UK
| | - David Linden
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Marianne Van den Bree
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences (DPMCN), School of Medicine, Cardiff University, Cardiff, UK
| | - Michael Owen
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences (DPMCN), School of Medicine, Cardiff University, Cardiff, UK
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK.,MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences (DPMCN), School of Medicine, Cardiff University, Cardiff, UK
| | - Adrian J Harwood
- Neuroscience and Mental Health Research Institute, Hadyn Ellis Building, Cathays, Cardiff, CF24 4HQ, UK. .,School of Bioscience, The Sir Martin Evans Building, Museum Ave, Cardiff, CF10 3AX, UK.
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6
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Frisk S, Wachtmeister A, Laurell T, Lindstrand A, Jäntti N, Malmgren H, Lagerstedt-Robinson K, Tesi B, Taylan F, Nordgren A. Detection of germline mosaicism in fathers of children with intellectual disability syndromes caused by de novo variants. Mol Genet Genomic Med 2022; 10:e1880. [PMID: 35118825 PMCID: PMC9000944 DOI: 10.1002/mgg3.1880] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown. Methods To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers). Results We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant. Conclusion By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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Affiliation(s)
- Sofia Frisk
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Alexandra Wachtmeister
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Laurell
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Hand Surgery, Södersjukhuset, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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7
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Li S, Wang W, Zhang D, Li W, Lund J, Kruse T, Mengel-From J, Christensen K, Tan Q. Differential regulation of the DNA methylome in adults born during the Great Chinese Famine in 1959-1961. Genomics 2021; 113:3907-3918. [PMID: 34600028 DOI: 10.1016/j.ygeno.2021.09.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/24/2021] [Accepted: 09/25/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Extensive epidemiological studies have established the association between exposure to early-life adversity and health status and diseases in adults. Epigenetic regulation is considered as a key mediator for this phenomenon but analysis on humans is sparse. The Great Chinese Famine lasting from 1958 to 1961 is a natural string of disasters offering a precious opportunity for elucidating the underlying epigenetic mechanism of the long-term effect of early adversity. METHODS Using a high-throughput array platform for DNA methylome profiling, we conducted a case-control epigenome-wide association study on early-life exposure to Chinese famine in 79 adults born during 1959-1961 and compared to 105 unexposed subjects born 1963-1964. RESULTS The single CpG site analysis of whole epigenome revealed a predominant pattern of decreased DNA methylation levels associated with fetal exposure to famine. Four CpG sites were detected with p < 1e-06 (linked to EHMT1, CNR1, UBXN7 and ESM1 genes), 16 CpGs detected with 1e-06 < p < 1e-05 and 157 CpGs with 1e-05 < p < 1e-04, with a predominant pattern of hypomethylation. Functional annotation to genes and their enriched biological pathways mainly involved neurodevelopment, neuropsychological disorders and metabolism. Multiple sites analysis detected two top-rank differentially methylated regions harboring RNF39 on chromosome 6 and PTPRN2 on chromosome 7, both showing epigenetic association with stress-related conditions. CONCLUSION Early-life exposure to famine could mediate DNA methylation regulations that persist into adulthood with broad impacts in the activities of genes and biological pathways. Results from this study provide new clues to the epigenetic embedding of early-life adversity and its impacts on adult health.
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Affiliation(s)
- Shuxia Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Weijing Wang
- Qingdao University School of Public Health, Qingdao, China
| | - Dongfeng Zhang
- Qingdao University School of Public Health, Qingdao, China
| | - Weilong Li
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark; Population Research Unit, Faculty of Social Sciences, University of Helsinki, Finland.
| | - Jesper Lund
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark; Digital Health & Machine Learning Research Group, Hasso Plattner Institute for Digital Engineering, Potsdam, Germany.
| | - Torben Kruse
- Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Jonas Mengel-From
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Kaare Christensen
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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8
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Jobic F, Lacot-Leriche E, Piton A, Le Moing AG, Mathieu-Dramard M, Costantini S, Morin G, Jedraszak G. Kleefstra syndrome: Recurrence in siblings due to a paternal mosaic mutation. Am J Med Genet A 2021; 185:3877-3883. [PMID: 34357686 DOI: 10.1002/ajmg.a.62448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 11/06/2022]
Abstract
Kleefstra syndrome (KS) is a rare autosomic dominant genetic disorder caused by euchromatic histone methyltransferase 1 (EHMT1) alterations. Patients mainly present with moderate to severe intellectual disability, a severe delay in/or absence of speech, autism spectrum disorder, childhood hypotonia, neuropsychiatric anomalies, and distinctive dysmorphic features. Here, we report the cases of a male and a female, two younger siblings of three, with asymptomatic parents. An EHMT1 new mutation was identified. Both presented with a typical core phenotype. Some specific features were noted, such as macrocephaly (previously reported) and enuresis (not yet described). Parental analysis identified the mutation in the mosaic state in the father. Reverse phenotyping enabled us to highlight the pauci phenotype features of inguinal hernia, azoospermia, and possible behavioral disorders. This allowed us to adapt his follow-up and genetic counseling for the family. Our three reported cases provide a new description of KS with an intragenic EHMT1 mutation, whereas in the literature most reported cases have EHMT1 deletions. Moreover, in the areas of next-generation sequencing and trio techniques with parental segregation, it is important to remain cautious about disregarding variants based on an autosomal recessive hypothesis.
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Affiliation(s)
- Florence Jobic
- Reference Center for Rare Diseases, Amiens-Picardy University Hospital, Amiens, France
| | - Emilie Lacot-Leriche
- Reference Center for Rare Diseases, Amiens-Picardy University Hospital, Amiens, France.,EA 7273 CRP-CPO, University of Picardy, Jules Verne, Amiens, France
| | - Amélie Piton
- Laboratory of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anne-Gaëlle Le Moing
- Department of Child Neurology, Amiens-Picardy University Hospital, Amiens, France
| | | | - Sara Costantini
- Reference Center for Rare Diseases, Amiens-Picardy University Hospital, Amiens, France
| | - Gilles Morin
- Genetics Laboratory, Amiens-Picardy University Hospital, Amiens, France
| | - Guillaume Jedraszak
- Genetics Laboratory, Amiens-Picardy University Hospital, Amiens, France.,EA 4666 HEMATIM - CURS, University of Picardy, Jules Verne, Amiens, France
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9
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Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder. Nat Commun 2021; 12:3750. [PMID: 34145229 PMCID: PMC8213845 DOI: 10.1038/s41467-021-23453-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Bipolar disorder is a severe mental illness characterized by recurrent manic and depressive episodes. To better understand its genetic architecture, we analyze ultra-rare de novo mutations in 354 trios with bipolar disorder. For germline de novo mutations, we find significant enrichment of loss-of-function mutations in constrained genes (corrected-P = 0.0410) and deleterious mutations in presynaptic active zone genes (FDR = 0.0415). An analysis integrating single-cell RNA-sequencing data identifies a subset of excitatory neurons preferentially expressing the genes hit by deleterious mutations, which are also characterized by high expression of developmental disorder genes. In the analysis of postzygotic mutations, we observe significant enrichment of deleterious ones in developmental disorder genes (P = 0.00135), including the SRCAP gene mutated in two unrelated probands. These data collectively indicate the contributions of both germline and postzygotic mutations to the risk of bipolar disorder, supporting the hypothesis that postzygotic mutations of developmental disorder genes may contribute to bipolar disorder. The significance of rare and de novo variants in bipolar disorder is not well understood. Here, the authors have analyzed whole exome/genome data from trios to identify deleterious de novo variants associated with bipolar disorder.
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10
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De Taevernier C, Meunier-Cussac S, Madigand J. First episode of psychosis in Kleefstra syndrome: a case report. Neurocase 2021; 27:227-230. [PMID: 34010111 DOI: 10.1080/13554794.2021.1905851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Kleefstra syndrome (KS) is a genetic syndrome caused by a haploinsufficiency of the EHMT1 gene and characterized by intellectual disability, language disorders, childhood hypotonia and distinct facial features. Only a few cases of first episode of psychosis in KS have already been reported. We describe a young female patient with KS who presented a first episode of psychosis. In a context of an initial diagnosis wavering and a lack of recommendations, this clinical observation illustrates the importance of psychiatric comorbidities and their diagnostic and therapeutic complexity in KS; with a need for multidisciplinary management considering its specific aspects and vulnerabilities.
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11
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A Novel WAC Loss of Function Mutation in an Individual Presenting with Encephalopathy Related to Status Epilepticus during Sleep (ESES). Genes (Basel) 2020; 11:genes11030344. [PMID: 32214004 PMCID: PMC7141116 DOI: 10.3390/genes11030344] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 01/10/2023] Open
Abstract
WAC (WW Domain Containing Adaptor With Coiled-Coil) mutations have been reported in only 20 individuals presenting a neurodevelopmental disorder characterized by intellectual disability, neonatal hypotonia, behavioral problems, and mildly dysmorphic features. Using targeted deep sequencing, we screened a cohort of 630 individuals with variable degrees of intellectual disability and identified five WAC rare variants: two variants were inherited from healthy parents; two previously reported de novo mutations, c.1661_1664del (p.Ser554*) and c.374C>A (p.Ser125*); and a novel c.381+2T>C variant causing the skipping of exon 4 of the gene, inherited from a reportedly asymptomatic father with somatic mosaicism. A phenotypic evaluation of this individual evidenced areas of cognitive and behavioral deficits. The patient carrying the novel splicing mutation had a clinical history of encephalopathy related to status epilepticus during slow sleep (ESES), recently reported in another WAC individual. This first report of a WAC somatic mosaic remarks the contribution of mosaicism in the etiology of neurodevelopmental and neuropsychiatric disorders. We summarized the clinical data of reported individuals with WAC pathogenic mutations, which together with our findings, allowed for the expansion of the phenotypic spectrum of WAC-related disorders.
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12
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Mossa A, Manzini MC. Molecular causes of sex-specific deficits in rodent models of neurodevelopmental disorders. J Neurosci Res 2019; 99:37-56. [PMID: 31872500 PMCID: PMC7754327 DOI: 10.1002/jnr.24577] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 11/02/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022]
Abstract
Neurodevelopmental disorders (NDDs) such as intellectual disability and autism spectrum disorder consistently show a male bias in prevalence, but it remains unclear why males and females are affected with different frequency. While many behavioral studies of transgenic NDD models have focused only on males, the requirement by the National Institutes of Health to consider sex as a biological variable has promoted the comparison of male and female performance in wild-type and mutant animals. Here, we review examples of rodent models of NDDs in which sex-specific deficits were identified in molecular, physiological, and/or behavioral responses, showing sex differences in susceptibility to disruption of genes mutated in NDDs. Haploinsufficiency in genes involved in mechanisms such as synaptic function (GABRB3 and NRXN1), chromatin remodeling (CHD8, EMHT1, and ADNP), and intracellular signaling (CC2D1A and ERK1) lead to more severe behavioral outcomes in males. However, in the absence of behavioral deficits, females can still present with cellular and electrophysiological changes that could be due to compensatory mechanisms or differential allocation of molecular and cellular functions in the two sexes. By contrasting these findings with mouse models where females are more severely affected (MTHFR and AMBRA1), we propose a framework to approach the study of sex-specific deficits possibly leading to sex bias in NDDs.
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Affiliation(s)
- Adele Mossa
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - M Chiara Manzini
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.,Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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13
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Jeon SJ, Gonzales EL, Mabunga DFN, Valencia ST, Kim DG, Kim Y, Adil KJL, Shin D, Park D, Shin CY. Sex-specific Behavioral Features of Rodent Models of Autism Spectrum Disorder. Exp Neurobiol 2018; 27:321-343. [PMID: 30429643 PMCID: PMC6221834 DOI: 10.5607/en.2018.27.5.321] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/08/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022] Open
Abstract
Sex is an important factor in understanding the clinical presentation, management, and developmental trajectory of children with neuropsychiatric disorders. While much is known about the clinical and neurobehavioral profiles of males with neuropsychiatric disorders, surprisingly little is known about females in this respect. Animal models may provide detailed mechanistic information about sex differences in autism spectrum disorder (ASD) in terms of manifestation, disease progression, and development of therapeutic options. This review aims to widen our understanding of the role of sex in autism spectrum disorder, by summarizing and comparing behavioral characteristics of animal models. Our current understanding of how differences emerge in boys and girls with neuropsychiatric disorders is limited: Information derived from animal studies will stimulate future research on the role of biological maturation rates, sex hormones, sex-selective protective (or aggravating) factors and psychosocial factors, which are essential to devise sex precision medicine and to improve diagnostic accuracy. Moreover, there is a strong need of novel strategies to elucidate the major mechanisms leading to sex-specific autism features, as well as novel models or methods to examine these sex differences.
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Affiliation(s)
- Se Jin Jeon
- Center for Neuroscience, Korea Institute of Science & Technology, Seoul 02792, Korea.,Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea
| | - Edson Luck Gonzales
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Darine Froy N Mabunga
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Schley T Valencia
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Do Gyeong Kim
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Yujeong Kim
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Keremkleroo Jym L Adil
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Dongpil Shin
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Donghyun Park
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea
| | - Chan Young Shin
- Department of Pharmacology and Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul 05029, Korea.,KU Open Innovation Center, Konkuk University, Seoul 05029, Korea
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14
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Abad C, Cook MM, Cao L, Jones JR, Rao NR, Dukes-Rimsky L, Pauly R, Skinner C, Wang Y, Luo F, Stevenson RE, Walz K, Srivastava AK. A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation. BIOLOGY 2018; 7:biology7020031. [PMID: 29794985 PMCID: PMC6023015 DOI: 10.3390/biology7020031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/20/2018] [Accepted: 05/21/2018] [Indexed: 12/17/2022]
Abstract
Deletions and mutations involving the Retinoic Acid Induced 1 (RAI1) gene at 17p11.2 cause Smith-Magenis syndrome (SMS). Here we report a patient with autism as the main clinical presentation, with some SMS-like features and a rare de novo RAI1 gene mutation, c.3440G > A (p.R1147Q). We functionally characterized the RAI1 p.R1147Q mutant protein. The mutation, located near the nuclear localization signal, had no effect on the subcellular localization of the mutant protein. However, similar to previously reported RAI1 missense mutations in SMS patients, the RAI1 p.R1147Q mutant protein showed a significant deficiency in activating in vivo transcription of a reporter gene driven by a BDNF (brain-derived neurotrophic factor) intronic enhancer. In addition, expression of other genes associated with neurobehavioral abnormalities and/or neurodevelopmental disorders were found to be altered in this patient. These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.
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Affiliation(s)
- Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami, FL 33136, USA.
| | - Melissa M Cook
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA.
| | - Lei Cao
- John P. Hussman Institute for Human Genomics, University of Miami, FL 33136, USA.
| | - Julie R Jones
- Molecular Diagnostic Laboratory, Greenwood Genetic Center, Greenwood, SC 29646, USA.
| | - Nalini R Rao
- John P. Hussman Institute for Human Genomics, University of Miami, FL 33136, USA.
| | - Lynn Dukes-Rimsky
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA.
| | - Rini Pauly
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA.
| | - Cindy Skinner
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA.
| | - Yunsheng Wang
- School of Computing, Clemson University, Clemson, SC 29634, USA.
| | - Feng Luo
- School of Computing, Clemson University, Clemson, SC 29634, USA.
| | - Roger E Stevenson
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA.
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, University of Miami, FL 33136, USA.
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, FL 33136, USA.
| | - Anand K Srivastava
- J. C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA.
- Department of Genetics and Biochemsitry, Clemson University, Clemson, SC 29634, USA.
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